Fears have intensified that BAE Systems is poised to axe potentially more than 1,000 jobs at its three British shipyards as work nears the end on an aircraft carrier project blighted by cost over-runs.

The defence contractor is thought to be close to ending months of speculation by clarifying the future workloads at its two Scottish yards on the Clyde – Govan and Scotstoun – and its Portsmouth site in southern England.

An announcement could be made later this week, possibly on Thursday, from both the company and the defence ministry.

BAE employs 3,200 staff at its two Scottish yards and a further 1,200 in its shipbuilding operations at Portsmouth. Some job losses could be offset by a contract to build the new Type 26 frigate.

Employees’ jobs are on the line as work draws to a close on the controversial project to build two Royal Navy aircraft carriers, where costs have almost doubled from the original budget of £3.7bn. The first of the ships is due for delivery in 2017.

It emerged earlier this week that the two carriers would now cost at least £800m more than previously expected, pushing the total cost up to £6.2bn – and that the latest cost over-runs would be shared on a 50:50 basis between the taxpayer and BAE.

Industry experts have speculated that BAE struck a more favourable deal than expected on apportioning the cost-overruns in return for a promise not to take the politically alarming decision of closing one of the yards.

The BBC reported last night that Govan would not close – despite fevered speculation in recent days, after BAE said it would decomission five cranes. The company stressed they had not been used since 2008.

BAE would only say on Tuesday night: “We continue to work closely with the Ministry of Defence to explore all possible options to determine how best to sustain the capability to deliver complex warships in the UK in the future. This work is ongoing and we are committed to keeping our employees and trade unions informed as it progresses.”